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First code dump
Signed-off-by: Nicola VIGANÒ <[email protected]> Signed-off-by: Henri Der Sarkissian <[email protected]>
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‎.github/ISSUE_TEMPLATE.md

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* PyRMLSeg version:
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* Python version:
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* Operating System:
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### Description
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Describe what you were trying to get done.
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Tell us what happened, what went wrong, and what you expected to happen.
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### What I Did
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```
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Paste the command(s) you ran and the output.
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If there was a crash, please include the traceback here.
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```

‎CHANGELOG.md

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Added
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- Linear relaxation of multi-levelset based segmentation
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- Total Variation (TV) and Laplacian (smoothness) based denoising
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- Estimation of the segmentation gray values
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- Refinement of the segmentation, based on the local reconstructed residual error (RRE)
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<!--
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### Fixed
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- <insert-bugs-fixed-not-in-a-release-yet>
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-->
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<!--
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## 0.1.0 - YYYY-MM-DD
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### Added
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- Initial release.
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-->
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[Unreleased]: https://www.github.com/cicwi/rmlseg/compare/v0.1.0...develop

‎CONTRIBUTING.rst

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.. highlight:: shell
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============
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Contributing
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============
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Contributions are welcome, and they are greatly appreciated! Every little bit
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helps, and credit will always be given.
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You can contribute in many ways:
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Types of Contributions
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----------------------
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Report Bugs
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~~~~~~~~~~~
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Report bugs at https://github.com/cicwi/rmlseg/issues.
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If you are reporting a bug, please include:
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* Your operating system name and version.
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* Any details about your local setup that might be helpful in troubleshooting.
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* Detailed steps to reproduce the bug.
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Fix Bugs
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~~~~~~~~
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Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
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wanted" is open to whoever wants to implement it.
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Implement Features
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~~~~~~~~~~~~~~~~~~
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Look through the GitHub issues for features. Anything tagged with "enhancement"
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and "help wanted" is open to whoever wants to implement it.
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Write Documentation
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~~~~~~~~~~~~~~~~~~~
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PyRMLSeg could always use more documentation, whether as part of the
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official PyRMLSeg docs, in docstrings, or even on the web in blog posts,
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articles, and such.
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Submit Feedback
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~~~~~~~~~~~~~~~
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The best way to send feedback is to file an issue at https://github.com/cicwi/rmlseg/issues.
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If you are proposing a feature:
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* Explain in detail how it would work.
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* Keep the scope as narrow as possible, to make it easier to implement.
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* Remember that this is a volunteer-driven project, and that contributions
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are welcome :)
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Get Started!
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------------
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Ready to contribute? Here's how to set up `rmlseg` for local development.
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1. Fork the `rmlseg` repo on GitHub.
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2. Clone your fork locally::
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$ git clone [email protected]:your_name_here/rmlseg.git
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3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
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$ mkvirtualenv rmlseg
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$ cd rmlseg/
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$ python setup.py develop
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4. Create a branch for local development::
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$ git checkout -b name-of-your-bugfix-or-feature
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Now you can make your changes locally.
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5. When you're done making changes, check that your changes pass flake8 and the
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tests, including testing other Python versions with tox::
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$ flake8 rmlseg tests
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$ python setup.py test or py.test
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$ tox
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To get flake8 and tox, just pip install them into your virtualenv.
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6. Commit your changes and push your branch to GitHub::
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$ git add .
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$ git commit -m "Your detailed description of your changes."
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$ git push origin name-of-your-bugfix-or-feature
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7. Submit a pull request through the GitHub website.
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Pull Request Guidelines
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-----------------------
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Before you submit a pull request, check that it meets these guidelines:
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1. The pull request should include tests.
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2. If the pull request adds functionality, the docs should be updated. Put
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your new functionality into a function with a docstring, and add the
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feature to the list in README.rst.
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3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
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https://travis-ci.org/cicwi/rmlseg/pull_requests
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and make sure that the tests pass for all supported Python versions.
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Tips
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----
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To run a subset of tests::
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$ python -m unittest tests.test_rmlseg
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Deploying
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---------
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A reminder for the maintainers on how to deploy.
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Make sure all your changes are committed (including an entry in HISTORY.rst).
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Then run::
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$ bumpversion patch # possible: major / minor / patch
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$ git push
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$ git push --tags
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Travis will then deploy to PyPI if tests pass.

‎LICENSE renamed to ‎LICENSE.md

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MIT License
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3-
Copyright (c) 2019 Computational Imaging, CWI
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Relaxed multi-levelset segmentation package, with tomographically consistent
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refinement.
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Copyright (c) 2019 Henri DER SARKISSIAN and Nicola VIGANÒ, Computational
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Imaging, CWI
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎MANIFEST.in

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include rmlseg/VERSION

‎Makefile

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.PHONY: clean clean-test clean-pyc clean-build docs help install_dev
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.DEFAULT_GOAL := help
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define BROWSER_PYSCRIPT
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import os, webbrowser, sys
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try:
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from urllib import pathname2url
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except:
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from urllib.request import pathname2url
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webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
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endef
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export BROWSER_PYSCRIPT
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define PRINT_HELP_PYSCRIPT
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import re, sys
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for line in sys.stdin:
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match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
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if match:
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target, help = match.groups()
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print("%-20s %s" % (target, help))
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endef
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export PRINT_HELP_PYSCRIPT
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BROWSER := python -c "$$BROWSER_PYSCRIPT"
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help:
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@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
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clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
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clean-build: ## remove build artifacts
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rm -fr build/
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rm -fr dist/
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rm -fr .eggs/
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find . -name '*.egg-info' -exec rm -fr {} +
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find . -name '*.egg' -exec rm -f {} +
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clean-pyc: ## remove Python file artifacts
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find . -name '*.pyc' -exec rm -f {} +
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find . -name '*.pyo' -exec rm -f {} +
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find . -name '*~' -exec rm -f {} +
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find . -name '__pycache__' -exec rm -fr {} +
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clean-test: ## remove test and coverage artifacts
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rm -fr .tox/
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rm -f .coverage
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rm -fr htmlcov/
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rm -fr .pytest_cache
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lint: ## check style with flake8
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flake8 rmlseg tests
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test: ## run tests quickly with the default Python
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python setup.py test
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test-all: ## run tests on every Python version with tox
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tox
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coverage: ## check code coverage quickly with the default Python
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coverage run --source rmlseg setup.py test
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coverage report -m
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coverage html
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$(BROWSER) htmlcov/index.html
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docs/.nojekyll:
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mkdir -p docs
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touch docs/.nojekyll
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docs: docs/.nojekyll install_dev ## generate Sphinx HTML documentation, including API docs
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rm -f doc_sources/rmlseg.rst
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rm -f doc_sources/modules.rst
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sphinx-apidoc -o doc_sources/ rmlseg
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make -C doc_sources clean
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make -C doc_sources html
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$(BROWSER) docs/index.html
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servedocs: docs ## compile the docs watching for changes
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watchmedo shell-command -p '*.rst' -c '$(MAKE) -C doc_sources html' -R -D .
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install: clean ## install the package to the active Python's site-packages
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python setup.py install
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install_dev:
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# https://stackoverflow.com/a/28842733
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pip install -e .[dev]
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conda_package:
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conda install conda-build -y
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conda build conda/

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